Package ffx.potential.nonbonded

Class VanDerWaalsForm

java.lang.Object

ffx.potential.nonbonded.VanDerWaalsForm

public class VanDerWaalsForm
extends Object

This class contains fields and methods for maintaining details of the van der Waals functional form.

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
static final double	DEFAULT_VDW_CUTOFF	The default van der Waals cut-off radius is 12.0 Angstroms.
static final double	DEFAULT_VDW_TAPER	The default van der Waals taper location is at 90% of the cut-off distance.
final double	delta	Second constant suggested by Halgren for the Buffered-14-7 potential.
VDWType.EPSILON_RULE	epsilonRule	Epsilon combining rule.
final double	gamma	First constant suggested by Halgren for the Buffered-14-7 potential.
VDWType.RADIUS_RULE	radiusRule	Radius combining rule.
VDWType.RADIUS_SIZE	radiusSize	Radius size in the parameter file (radius or diameter).
VDWType.RADIUS_TYPE	radiusType	Radius type in the parameter file (R-Min or Sigma).
protected double	scale12	Define scale factors between 1-2 atoms.
protected double	scale13	Define scale factors between 1-3 atoms.
protected double	scale14	Define scale factors between 1-4 atoms.
VDWType.VDW_TYPE	vdwType	van der Waals functional form.

Constructor Summary

Constructors

Constructor	Description
VanDerWaalsForm(ForceField forceField)	Constructor for VanDerWaalsForm.

Method Summary

Modifier and Type	Method	Description
static double	getCombinedEps(double ei, double ej, double ri, double rj, VDWType.EPSILON_RULE epsilonRule)	Get the combined EPS value.
double	getCombinedEps(int class1, int class2)	Return the combined well depth (kcal/mol)
double	getCombinedEps14(int class1, int class2)	Return the combined well depth (kcal/mol) for special 1-4 interactions
double	getCombinedInverseRmin(int class1, int class2)	Return the combined inverse Rmin value (1/Rmin).
double	getCombinedInverseRmin14(int class1, int class2)	Return the combined inverse Rmin value (1/Rmin) for special 1-4 interactions.
static double	getCombinedRadius(double ri, double rj, VDWType.RADIUS_RULE radiusRule)	Get the combined radius value.
double[]	getEps()	Return the eps value for each class.
double[]	getRmin()	Return the Rmin value for each class.
double	getScale14()	Getter for the field scale14.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

DEFAULT_VDW_TAPER

public static final double DEFAULT_VDW_TAPER

The default van der Waals taper location is at 90% of the cut-off distance.

See Also:

• Constant Field Values

DEFAULT_VDW_CUTOFF

public static final double DEFAULT_VDW_CUTOFF

The default van der Waals cut-off radius is 12.0 Angstroms.

See Also:

• Constant Field Values

gamma

@FFXProperty(name="halgren-gamma",
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="0.12",
             description="Sets the value of the gamma parameter in Halgren\u2019s buffered 14-7 vdw potential energy functional form.\nIn the absence of the gamma-halgren property, a default value of 0.12 is used.\"\n")
public final double gamma

First constant suggested by Halgren for the Buffered-14-7 potential.

delta

@FFXProperty(name="halgren-delta",
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="0.07",
             description="Sets the value of the delta parameter in Halgren\u2019s buffered 14-7 vdw potential energy functional form.\nIn the absence of the delta-halgren property, a default value of 0.07 is used.\n")
public final double delta

Second constant suggested by Halgren for the Buffered-14-7 potential.

vdwType

@FFXProperty(name="vdwtype",
             clazz=java.lang.String.class,
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="LENNARD-JONES",
             description="[LENNARD-JONES / BUFFERED-14-7]\nSets the functional form for the van der Waals potential energy term.\nThe text modifier gives the name of the functional form to be used.\nThe default in the absence of the vdwtype keyword is to use the standard two parameter Lennard-Jones function.\n")
public VDWType.VDW_TYPE vdwType

van der Waals functional form.

epsilonRule

@FFXProperty(name="epsilonrule",
             clazz=java.lang.String.class,
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="GEOMETRIC",
             description="[GEOMETRIC / HHG / W-H]\nSelects the combining rule used to derive the epsilon value for van der Waals interactions.\nThe default in the absence of the epsilonrule keyword is to use the geometric mean of the\nindividual epsilon values of the two atoms involved in the van der Waals interaction.\n")
public VDWType.EPSILON_RULE epsilonRule

Epsilon combining rule.

radiusRule

@FFXProperty(name="radiusrule",
             clazz=java.lang.String.class,
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="ARITHMETIC",
             description="[ARITHMETIC / GEOMETRIC / CUBIC-MEAN]\nSets the functional form of the radius combining rule for heteroatomic van der Waals potential energy interactions.\nThe default in the absence of the radiusrule keyword is to use the arithmetic mean combining rule to get radii for heteroatomic interactions.\n")
public VDWType.RADIUS_RULE radiusRule

Radius combining rule.

radiusSize

@FFXProperty(name="radiussize",
             clazz=java.lang.String.class,
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="RADIUS",
             description="[RADIUS / DIAMETER]\nDetermines whether the atom size values given in van der Waals parameters read from\nVDW keyword statements are interpreted as atomic radius or diameter values.\nThe default in the absence of the radiussize keyword is to assume that vdw size parameters are given as radius values.\n")
public VDWType.RADIUS_SIZE radiusSize

Radius size in the parameter file (radius or diameter).

radiusType

@FFXProperty(name="radiustype",
             clazz=java.lang.String.class,
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="R-MIN",
             description="[R-MIN / SIGMA]\nDetermines whether atom size values given in van der Waals parameters read from VDW keyword\nstatements are interpreted as potential minimum (Rmin) or LJ-style sigma values.\nThe default in the absence of the radiustype keyword is to assume that vdw size parameters are given as Rmin values.\n")
public VDWType.RADIUS_TYPE radiusType

Radius type in the parameter file (R-Min or Sigma).

scale12

@FFXProperty(name="vdw-12-scale",
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="0.0",
             description="Provides a multiplicative scale factor that is applied to van der Waals potential\ninteractions between 1-2 connected atoms, i.e., atoms that are directly bonded.\nThe default value of 0.0 is used to omit 1-2 interactions,\nif the vdw-12-scale property is not given in either the parameter file or the property file.\n")
protected double scale12

Define scale factors between 1-2 atoms.

scale13

@FFXProperty(name="vdw-13-scale",
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="0.0",
             description="Provides a multiplicative scale factor that is applied to van der Waals potential\ninteractions between 1-3 connected atoms, i.e., atoms separated by two covalent bonds.\nThe default value of 0.0 is used to omit 1-3 interactions, if the vdw-13-scale property\nis not given in either the parameter file or the property file.\n")
protected double scale13

Define scale factors between 1-3 atoms.

scale14

@FFXProperty(name="vdw-14-scale",
             propertyGroup=VanDerWaalsFunctionalForm,
             defaultValue="1.0",
             description="Provides a multiplicative scale factor that is applied to van der Waals potential\ninteractions between 1-4 connected atoms, i.e., atoms separated by three covalent bonds.\nThe default value of 1.0 is used, if the vdw-14-scale keyword is not given in either\nthe parameter file or the property file.\n")
protected double scale14

Define scale factors between 1-4 atoms.

Constructor Details

VanDerWaalsForm

public VanDerWaalsForm(ForceField forceField)

Constructor for VanDerWaalsForm.

Parameters:

forceField - a ForceField object.

Method Details

getCombinedEps

public static double getCombinedEps(double ei,
 double ej,
 double ri,
 double rj,
 VDWType.EPSILON_RULE epsilonRule)

Get the combined EPS value.

Parameters:

ei - The eps value of the first atom.

ej - The eps value of the second atom.

ri - The radius of the first atom.

rj - The radius of the second atom.

epsilonRule - The epsilon rule to use.

Returns:

The combined eps value.

getCombinedRadius

public static double getCombinedRadius(double ri,
 double rj,
 VDWType.RADIUS_RULE radiusRule)

Get the combined radius value.

Parameters:

ri - The radius of the first atom.

rj - The radius of the second atom.

radiusRule - The radius combining rule to use.

Returns:

The combined radius value.

getCombinedEps

public double getCombinedEps(int class1,
 int class2)

Return the combined well depth (kcal/mol)

Parameters:

class1 - Class for atom 1.

class2 - Class for atom 2.

Returns:

Combined Eps.

getCombinedEps14

public double getCombinedEps14(int class1,
 int class2)

Return the combined well depth (kcal/mol) for special 1-4 interactions

Parameters:

class1 - Class for atom 1.

class2 - Class for atom 2.

Returns:

Combined Eps.

getCombinedInverseRmin

public double getCombinedInverseRmin(int class1,
 int class2)

Return the combined inverse Rmin value (1/Rmin).

Parameters:

class1 - Class for atom 1.

class2 - Class for atom 2.

Returns:

Combined inverse Rmin.

getCombinedInverseRmin14

public double getCombinedInverseRmin14(int class1,
 int class2)

Return the combined inverse Rmin value (1/Rmin) for special 1-4 interactions.

Parameters:

class1 - Class for atom 1.

class2 - Class for atom 2.

Returns:

Combined inverse Rmin.

getEps

public double[] getEps()

Return the eps value for each class.

Returns:

Returns the eps array.

getRmin

public double[] getRmin()

Return the Rmin value for each class.

Returns:

Returns the Rmin array.

getScale14

public double getScale14()

Getter for the field scale14.

Returns:

a double.